The complete plastid genome of Abrus pulchellus subsp. mollis (Leguminosae): a medicinal plant in Southern China

Abstract The subspecies Abrus pulchellus subsp. mollis exhibits pharmacological properties akin to the traditional Chinese medicinal plant Abri Herba (A. pulchellus subsp. cantoniensis (Hance) Verdc.). In this report, we unveil the plastid genome of A. pulchellus subsp. mollis. The genome spans 156,322 base pairs (bp), comprising a large single-copy (LSC) region of 86,633 bp, a small single-copy (SSC) region of 18,219 bp, and two distinct inverted repeat regions (IRs) of 25,735 bp each. Annotation process cataloged a total of 111 genes within this genome, including 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The overall guanine-cytosine (GC) content of the plastome is 35.5%. Phylogenetic analysis utilizing maximum-likelihood (ML) based on 16 complete plastid genomes reveals a close clustering of three Abrus taxa, namely A. pulchellus subsp. mollis, A. pulchellus subsp. cantoniensis, and A. precatorius. Notably, A. pulchellus subsp. cantoniensis clusters with A. precatorius as a sister group, distinct from A. pulchellus subsp. mollis. These findings highlight significant differences between the plastid genomes of the two subspecies, laying the foundation for future research on the identification of medicinal herbs and germplasm resources related to these subspecies.


Introduction
The Abrus Adans.(Leguminosae) encompasses approximately 17 species globally, distributed across the tropical and subtropical region of the old world to the Southwest Pacific (https://powo.science.kew.org).In China, two species, Abrus precatorius L. and A. pulchellus Wallich ex Thwaites are documented within this genus (Bao and Gilbert 2010).Additionally, A. pulchellus is differentiated into three subspecies (Bao and Gilbert Figure 1.The species reference images of Abrus pulchellus subsp.mollis.The photographs were taken by Puyue Ouyang at Guangdong Food and Drug Vocational College.The species' indumentum is at least partially ferruginous, predominantly erect, and often gray on leaves.If the indumentum is gray, the leaflets are approximately 3 cm in length, and the pod is 3.5-4.9cm in length. CONTACT Cai-Yun Zhang zhangcaiy@126.comGuangdong Food and Drug Vocational College, Guangzhou, China Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2383684.2010).The subspecies A. pulchellus subsp.cantoniensis (Hance) Verdc., colloquially known as Abri Herba or 'Jigucao' in Chinese (Chinese Pharmacopoeia Commission 2020), is widely utilized in traditional Chinese medicine for treating hepatitis and liver fibrosis and as a component in herbal teas and soups in southern China (Shen et al. 2021).Conversely, Abrus pulchellus subsp.mollis (Hance) Verdc.1871 shares pharmaceutical properties and is commonly used as Abri Herba in practical applications.Morphologically, these two subspecies are indistinguishable.This study presents the plastid genome of A. pulchellus subsp.mollis to facilitate future authentication and quality control of the herbal medicine.

Results
The high coverage depth (the average coverage was 1427�, Figure S1) of the resulting plastome of A. pulchellus subsp.mollis demonstrates the accuracy of the plastome we assembled.The plastome measures 156,322 base pairs (bp), featuring a large single-copy (LSC) region of 86,633 bp, a small single-copy (SSC) region of 18,219 bp, and two distinct inverted repeat regions (IRs) of 25,735 bp each (Figure 2).In total, 111 genes were annotated, including 77 CDS, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes.Notably, 17 genes are duplicated due to their location within the IR regions.Fifteen genes, such as rpoC1, atpF, rps16, harbor a single intron, while clpP possesses two introns.The rps12 is identified as a trans-splicing gene, comprising three exons and one intron, with one exon situated in LSC region, separate from the remaining segments in the IR regions.The gene structure maps of cis-and trans-splicing gene are shown in Figures S2 and S3.The overall guanine-cytosine (GC) content of the plastome stands at 35.5%, with the LSC, SSC, and IR regions having GC contents of 32.8, 28.8, and 42.4%, respectively.
The aligned matrix, consisting of 76 conserved CDS derived from 16 complete plastid genomes (including the newly sequenced plastome presented in this study) was conducted using MAFFT v7.490 (Katoh and Standley 2013).This matrix was used for ML tree construction.Our analysis revealed a cohesive clustering of the three Abrus taxa, specifically A. pulchellus subsp.mollis, A. pulchellus subsp.cantoniensis, and A. precatorius, as depicted in Figure 3. Notably, A. pulchellus subsp.cantoniensis formed a sister group with A. precatorius, but not to the subspecies A. pulchellus subsp.mollis (Figure 3).

Discussion and conclusions
The subspecies A. pulchellus subsp.mollis has garnered significant interest due to its profound medicinal properties in southern China.However, prior research has predominantly concentrated on its medicinal constituents, as noted by Hu et al. (2019).Morphologically, this subspecies bears resemblance to A. pulchellus subsp.cantoniensis, yet previous phylogenetic data were limited.For instance, only a scant number of molecular fragments from A. pulchellus subsp.mollis are accessible on NCBI (https://www.ncbi.nlm.nih.gov/nuccore/), encompassing a few plastid fragments such as rbcL and matK.Consequently, the precise phylogenetic relationships among the two subspecies of A. pulchellus and their closely related taxa within the same genus remain obscure.
With the advent of advanced sequencing technologies and the continual evolution of plastid genome assembly and analysis methodologies, the plastome has emerged as a pivotal instrument for current phylogenetic plant studies and the authentication of Chinese medicinal herbs, as highlighted by Chen et al. (2023) and Guo et al. (2023).This study marks the inaugural report on the structure and genetic composition of the plastome of A. pulchellus subsp.mollis, alongside a preliminary reconstruction of its phylogenetic ties with closely related taxa.The phylogenetic analysis of the plastid genomes reveals that A. pulchellus subsp.cantoniensis clusters in a sister group with A. precatorius and subsequently forms a clade with A. pulchellus subsp.mollis.These finding underscore substantial differences between the plastid genomes of the two subspecies, thereby establishing a groundwork for future research on the identification of medicinal herbs and germplasm resources pertaining to these subspecies.

Figure 2 .
Figure 2. Gene map of the plastid genome of Abrus pulchellus subsp.mollis.Genes outside the circle are transcribed counterclockwise, and genes inside the circle are transcribed clockwise.The gray graph in the inner circle shows the GC content with 50% threshold line.